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CHECK report for ecolitk on machv2

This page was generated on 2020-10-17 11:58:25 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ecolitk PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 525/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ecolitk 1.60.0
Laurent Gautier
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/ecolitk
Branch: RELEASE_3_11
Last Commit: cdf7a51
Last Changed Date: 2020-04-27 14:08:59 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ecolitk
Version: 1.60.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ecolitk.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ecolitk_1.60.0.tar.gz
StartedAt: 2020-10-17 00:47:11 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 00:48:04 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 53.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ecolitk.Rcheck
Warnings: 1

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ecolitk.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ecolitk_1.60.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/ecolitk.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ecolitk/DESCRIPTION’ ... OK
* this is package ‘ecolitk’ version ‘1.60.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ecolitk’ can be installed ... WARNING
Found the following significant warnings:
  Note: possible error in 'strsplit(line, "\t", ': unused argument (extended = TRUE) 
See ‘/Users/biocbuild/bbs-3.11-bioc/meat/ecolitk.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘graph’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.buildGENEPRODFUN: possible error in strsplit(line, "\t", extended =
  TRUE): unused argument (extended = TRUE)
* checking Rd files ... NOTE
prepare_Rd: multiFun.Rd:16-18: Dropping empty section \details
prepare_Rd: polar2xy.Rd:28-33: Dropping empty section \value
prepare_Rd: polygonChrom.Rd:59: Dropping empty section \seealso
prepare_Rd: wstringapply.Rd:24-25: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/ecolitk.Rcheck/00check.log’
for details.



Installation output

ecolitk.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ecolitk
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘ecolitk’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
Note: possible error in 'strsplit(line, "\t", ': unused argument (extended = TRUE) 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ecolitk)

Tests output


Example timings

ecolitk.Rcheck/ecolitk-Ex.timings

nameusersystemelapsed
ecoli.data0.1540.0160.170
ecoligenome.operon0.1320.0080.140
linkedmultiget0.0890.0080.096
multiFun000
pointsCircle0.1100.0140.124
polar2xy0.0260.0030.028
polygonChrom0.0860.0070.093